[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Tue Oct 18 13:09:22 CEST 2011

James Starlight wrote:
> Dear Justin,
> Indeed I didnt take into account square degree so all values presented 
> in the tutorial exactly true so this was exactly my mistake. :(
> After some iterations I've obtained value for S per lipid beetween 
> 0.65-0.71 A^2.  This is the example of the system wich I've obtained 
> after solvation and futher minimization. 
> http://www.sendspace.com/file/h6urhq  It looks good. :)  By the way I'd 
> like to know about correct value for the S per protein ? Where I can 
> obtain such information for my protein ? ( e.g for big proteins such 
> receptors and channels )

Such information depends on whether there is experimental evidence for the 
protein you're looking for.

> The error with GenBox was due to the big vdv R for the carbons. It's 
> intresting that I couldnt increase this value mush as 1.2. But my 
> finally system didnt consist of some water within the membrane so I 
> supose that it's good.
> Now my system on the stage of the equilibtation so I have not any 
> questions yet but I only wounder to know about teqnique of the force 
> fied preparation for the membrane protein simulation.
> In this work I've done this step in accordance with the tutorial. On the 
> last stage I've copied  gromos53a6_lipid.ff directory in $GMXLIB so now 
> I can use it in pdb2gmx for instance. 
> But when I've tried to make gro and top files for my  lipid.pdb via 
> pdb2gmx I've obtained errors that Residue 'DPP' not found in residue 
> topology database so I think that in addition to the operations wich 
> I've already done I should also make some changes in the
> /gromos53a6_lipid.ff/aminoacids.hdb
>  ./gromos53a6_lipid.ff/aminoacids.n.tdb
>  ./gromos53a6_lipid.ff/aminoacids.c.tdb
> shouldn't I?

pdb2gmx is not suited for building topologies of multi-molecule, heterogeneous 
systems like solvated membranes.  You may be able to get a topology, but it will 
be a redundant mess.  Follow the protocol in the tutorial; it avoids these 
issues in the most streamlined way possible.  If you need a topology of a new 
lipid, create an .rtp entry (if one does not exist already) and run pdb2gmx on a 
single lipid molecule.  You can then #include the new .itp file in your system 

> Finally, I've heard that there are already pre-build force fields for 
> the membrane smulation. E.g  I've heard that there is some modified 
> CHARMM ff wich gave good results in simulation. Do you know something 
> about this?

Various CHARMM parameter sets exist.  CHARMM27 is built into the Gromacs 4.5.x 
series, and CHARMM36 is available from the User Contributions section of the 


> Thank you for your help,
> James


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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